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comparison SAM_Refiner_Gal.xml @ 1:b68f7e37e70a draft default tip

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author degregory
date Mon, 13 Sep 2021 14:14:20 +0000
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0:22e3f843f1db 1:b68f7e37e70a
1 <tool id="SAM_Refiner" name="SAM Refiner" version="1.0">
2 <description>Provides variant information from mapped reads</description>
3 <command>
4 python '${__tool_directory__}/SAM_Refiner_Gal.py' -r $ref -S $samfile --min_samp_abund $minsampabund --min_count $mincount --ntabund $ntab --max_dist $maxdist --max_covar $maxcov
5 #if $use_count
6 --use_count 1
7 #else
8 --use_count 0
9 #end if
10 #if $seqs
11 -o1 $out_file1
12 #else
13 --seq 0
14 #end if
15 #if $indels
16 -o2 $out_file2
17 #else
18 --indel 0
19 #end if
20 #if $ntcalls:
21 -o3 $out_file3
22 #else
23 --nt_call 0
24 #end if
25 #if $covars
26 -o4 $out_file4
27 #else
28 --covar 0
29 #end if
30 #if $chimrm
31 -o5 $out_file5 --alpha $alpha --foldab $foldab
32 #else
33 --chim_rm 0
34 #end if
35 #if $covdec
36 -o6 $out_file6 --beta $beta --autopass $pass
37 #else
38 --deconv 0
39 #end if
40 #if $ntvar
41 --ntvar 1
42 -o7 $out_file7
43 #end if
44 #if $AArep
45 --AAreport 1
46 #else
47 --AAreport 0
48 #end if
49 #if $MNP
50 --AAcodonasMNP 1
51 #else
52 --AAcodonasMNP 0
53 #end if
54 #if $redist
55 --redist 1
56 #else
57 --redist 0
58 #end if
59 --samp '$samp'
60 #if $WGS
61 --wgs 1
62 #else
63 --wgs 0
64 #end if
65 </command>
66 <inputs>
67 <param format="fasta" name="ref" type="data" label="Reference fasta" />
68 <param format="sam" name="samfile" type="data" label="SAM file to be processed" />
69 <param name="samp" type="text" value="Sample" label="Sample Title" />
70 <param name="use_count" type="boolean" checked="false" label="Use read count in fasta id line (must have format id-count or id=count)" />
71 <param name="seqs" type="boolean" checked="true" label="Output Sequence TSV" />
72 <param name="indels" type="boolean" checked="true" label="Output Indel TSV" />
73 <param name="ntcalls" type="boolean" checked="true" label="Output NT Call TSV" />
74 <param name="ntvar" type="boolean" checked="true" label="Output file with only variant NT Calls TSV" />
75 <param name="covars" type="boolean" checked="true" label="Output Covariant TSV" />
76 <param name="chimrm" type="boolean" checked="true" label="Output Chimeras Removed TSV, requires Sequence TSV output" />
77 <param name="covdec" type="boolean" checked="true" label="Output Covariant Deconvolution TSV, requires Sequence and Covariant TSV outputs" />
78 <param name="WGS" type="boolean" checked="false" label="Use Whole Genome Sequencing Mode, disables chimera removal outputs, reports sequences with start and end positions" />
79 <param name="mincount" type="integer" value="5" min="1" max="20000" label="Minimum number of counts for an output line" />
80 <param name="minsampabund" type="float" value=".001" min="0" max=".5" label="Minimum abundance for an output line" />
81 <param name="ntab" type="float" value=".001" min="0" max=".5" label="Minimum abundance for an NT call line variant to be reported" />
82 <param name="maxdist" type="integer" value="20" min="1" max="40" label="Maximum distance from reference for a sequence to be included in the Covariant output processing (High values may cause memory/computational errors, reduce to avoid)" />
83 <param name="maxcov" type="integer" value="8" min="1" max="40" label="Maximum number of polymorphisms to report in each line of the Covariant output" />
84 <param name="AArep" type="boolean" checked="true" label="Report Amino Acids as if reference is an inframe ORF. If the reference isn't an in frame ORF, this should be disabled" />
85 <param name="MNP" type="boolean" checked="true" label="Report multiple nucleotide changes in a single codon as a single polymorphism, requires reporting of Amino Acids" />
86 <param name="redist" type="boolean" checked="true" label="Redistribute counts from chimeric sequecnes to parents in Chimeras Removed Output" />
87 <param name="alpha" type="float" value="1.2" min=".1" max="10" label="Modifier for chim_rm chimera checking, default 1.2. Higher = more sensitive, more false chimeras removed; lower = less sensitive, fewer chimeras removed" />
88 <param name="foldab" type="float" value="1.8" min="0" max="20" label="Threshold for potential parent / chimera abundance ratio for chim_rm; default is 1.8" />
89 <param name="beta" type="float" value="1" min=".1" max="4" label="Modifier for covar pass checking, default 1. Higher = more sensitive, more failed checks; lower = less sensitive, fewer failed checks" />
90 <param name="pass" type="float" value=".3" min=".1" max="4" label="Threshold for a sequence to automatically pass the covar pass checking" />
91 </inputs>
92
93 <outputs>
94 <data format="TSV" name="out_file1" label="${tool.name} on ${on_string}: sequences" />
95 <data format="TSV" name="out_file2" label="${tool.name} on ${on_string}: indels" />
96 <data format="TSV" name="out_file3" label="${tool.name} on ${on_string}: nt calls" />
97 <data format="TSV" name="out_file4" label="${tool.name} on ${on_string}: covariants" />
98 <data format="TSV" name="out_file5" label="${tool.name} on ${on_string}: chimeras removed" />
99 <data format="TSV" name="out_file6" label="${tool.name} on ${on_string}: covariant deconvolution" />
100 <data format="TSV" name="out_file7" label="${tool.name} on ${on_string}: variant nt calls" />
101 </outputs>
102
103 <tests>
104 <test>
105 <param name="ref" value="SAM_Refiner_test_ref.fa"/>
106 <param name="samfile" value="SAM_Refiner_test_sam.sam"/>
107 <output name="out_file1" file="SAM_Refiner_test_seqs.tsv"/>
108 <output name="out_file2" file="SAM_Refiner_test_indels.tsv"/>
109 <output name="out_file3" file="SAM_Refiner_test_nc_calls.tsv"/>
110 <output name="out_file4" file="SAM_Refiner_test_covars.tsv"/>
111 </test>
112 </tests>
113
114 <help>
115 SAM Refiner provides variant information from mapped reads in a SAM file. If you use this tool, please reference Gregory, D.A.; Wieberg, C.G.; Wenzel, J.; Lin, C.-H.; Johnson, M.C. Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner. Viruses 2021, 13, 1647. https://doi.org/10.3390/v13081647
116
117
118 </help>
119
120 </tool>